Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java
===================================================================
--- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java (revision 161)
+++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java (revision 173)
@@ -26,17 +26,17 @@
         ClassLink classLink;
         List<ClassLink> path;
-        boolean converge;
+        //boolean converge;
         
         public LinkAndPath(ClassLink classLink, List<ClassLink> path){
            this.classLink = classLink;
            this.path = path;
-           this.converge = false;
-        }
-        
-        public LinkAndPath(ClassLink classLink, List<ClassLink> path, String originalClassURI, boolean converge){
+           //this.converge = false;
+        }
+        
+        public LinkAndPath(ClassLink classLink, List<ClassLink> path, String originalClassURI){
            this.classLink = classLink;
            this.path = path;
            this.originalClassURI = originalClassURI;
-           this.converge = converge;
+           //this.converge = converge;
         }
     }
@@ -87,5 +87,5 @@
         List<List<ClassLink>> paths = new ArrayList<>();
         List<LinkAndPath> lp = new LinkedList<>();
-        lp.add(new LinkAndPath(new ClassLink("",startClass,null,Direction.both,0,0,0,0,0,false,false), new LinkedList<ClassLink>(), "", false));
+        lp.add(new LinkAndPath(new ClassLink("",startClass,null,Direction.both,0,0,0,0,0,false,false), new LinkedList<ClassLink>(), ""));
         try{
           for ( int i = 0; i < nsteps; i++ ){
@@ -94,6 +94,12 @@
               while ( lit.hasNext() ){
                   LinkAndPath crrlp = lit.next();
+                  /*if ( crrlp.classLink.getLinkedClassURI().equals("http://www.biopax.org/release/biopax-level3.owl#Pathway") ){
+                      System.out.println("here!");
+                  }*/
                   ClassLink[] classLinks = rdfsa.getNextClass(null, crrlp.classLink.getLinkedClassURI(), limit, countLinks);
                   for ( int j = 0 ; j < classLinks.length; j++ ){
+                      /*if ( classLinks[j].getLinkedClassURI().endsWith("http://www.biopax.org/release/biopax-level3.owl#BiochemicalReaction") ){
+                          ClassLink cltmp = classLinks[j];
+                      }*/
                       List<ClassLink> crrpath = new LinkedList<>(crrlp.path);
                       crrpath.add(classLinks[j]);
@@ -118,6 +124,10 @@
                           }
                       }
-                      
-                      nextlp.add(new LinkAndPath(classLinks[j], crrpath, crrlp.classLink.getLinkedClassURI(), false));
+                      /*
+                      if ( classLinks[j].getDirection() != Direction.reverse ){
+                         System.out.println("here b"); 
+                      }*/
+
+                      nextlp.add(new LinkAndPath(classLinks[j], crrpath, crrlp.classLink.getLinkedClassURI()));
                   }
               }
Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/AcquiredStructureAnalyzer.java
===================================================================
--- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/AcquiredStructureAnalyzer.java (revision 133)
+++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/AcquiredStructureAnalyzer.java (revision 173)
@@ -35,20 +35,23 @@
 	
 	public static void main(String[] args) throws Exception{
-		JenaModelGenerator jmGene = new JenaModelGenerator("c:\\temp\\reactomeF18s.ttl");
+
+		JenaModelGenerator jmGene = new JenaModelGenerator("c:\\temp\\biosamplesF11.ttl");
+//		JenaModelGenerator jmGene = new JenaModelGenerator("c:\\temp\\reactomeF18s.ttl");
 		AcquiredStructureAnalyzer impl 
 			= new AcquiredStructureAnalyzer(jmGene.getEndpointURI(), jmGene.getGraphURIs(), jmGene.getModel());
-//		System.out.println("--------------------------");
-//		SClass[] scs = impl.getOWLClasses(null, null, null, true);
-//		System.out.println("list classes:---------------");
-//		for(SClass sc: scs){
-//			System.out.println(sc.toString());
+
+		System.out.println("--------------------------");
+		SClass[] scs = impl.getOWLClasses(null, null, null, true);
+		System.out.println("list classes:---------------");
+		for(SClass sc: scs){
+			System.out.println(sc.toString());
+		}
+		System.out.println("--------------------------");
+		
+//		ClassLink[] cls = impl.getNextClass(null,"http://www.biopax.org/release/biopax-level3.owl#Protein",100,true );
+//		for(ClassLink cl: cls){
+//			System.out.println(cl.toString());
 //		}
 //		System.out.println("--------------------------");
-		
-		ClassLink[] cls = impl.getNextClass(null,"http://www.biopax.org/release/biopax-level3.owl#Protein",100,true );
-		for(ClassLink cl: cls){
-			System.out.println(cl.toString());
-		}
-		System.out.println("--------------------------");
 		
 	}
@@ -217,5 +220,5 @@
 		queryStr.append(" {");
 		queryStr.append(" ?cr <").append(URICollection.PROPERTY_SB_OBJECT_CLASS).append("> <" + originClass + ">. \n");
-		queryStr.append(" ?cr <").append(URICollection.PROPERTY_SB_SUBJECT_CLASS).append("> ?d. \n");
+		queryStr.append(" ?cr <").append(URICollection.PROPERTY_SB_SUBJECT_CLASS).append("> ?c. \n");
 		queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_DISTINCT_SUBJECTS).append("> ?numLnkInsEnd. \n");
 		queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_DISTINCT_OBJECTS).append("> ?numLnkInsStart. \n");
@@ -277,9 +280,9 @@
 				if(ccls != null && dcls == null ){
 					// direction forward
-					direction = Direction.forward;
+					direction = Direction.reverse;
 					clsURI = ccls.getURI();
 				}else{
 					if( ccls == null && dcls != null ){
-						direction = Direction.reverse;
+						direction = Direction.forward;
 						clsURI = dcls.getURI();
 					}else{